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Título: | Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera |
Autor: | Greco, Mattia CSIC ORCID; Morard, Raphaël; Darling, Kate; Kucera, Michal | Palabras clave: | Planktonic foraminifera Protists SSU rDNA Intra-individual variability Sequence polymorphism |
Fecha de publicación: | abr-2023 | Editor: | PeerJ | Citación: | PeerJ 11: e15255 (2023) | Resumen: | Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms and distribution of this phenomenon within a microbial group are rarely explored. Here, we investigate the intragenomic variability in 33 species of planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms are common among planktonic foraminifera species, but the number of polymorphic sites significantly differs among clades. With our molecular simulations, we could assess that most of these mutations are located in paired regions that do not affect the secondary structure of the SSU fragment. Finally, by mapping the number of polymorphic sites on the phylogeny of the clades, we were able to discuss the evolution and potential sources of intragenomic variability in planktonic foraminifera, linking this trait to the distinctive nuclear and genomic dynamics of this microbial group | Descripción: | 17 pages, 4 figures, supplemental information https://doi.org/10.7717/peerj.15255/supp-1.-- Data Availability: The following information was supplied regarding data availability: The accession numbers of the sequences are available in Table S1. The data tables and phylogenetic trees used for the analyses are available at FigShare: Greco, Mattia (2023): Supporting data to ‘Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera’. figshare. Dataset. https://doi.org/10.6084/m9.figshare.21316374.v1 The code used to generate the figures is available at GitHub and Zenodo: https://github.com/MatGreco90/IG_variability_planktonic_foraminifera Mattia Greco. (2023). MatGreco90/IG_variability_planktonic_foraminifera: zenodo_release (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.7797515 | Versión del editor: | https://doi.org/10.7717/peerj.15255 | URI: | http://hdl.handle.net/10261/330322 | DOI: | 10.7717/peerj.15255 | E-ISSN: | 2167-8359 |
Aparece en las colecciones: | (ICM) Artículos |
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Greco_et_al_2023_suppl_table_1.txt | 5 MB | Text | Visualizar/Abrir |
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